Abstract
The DNA of higher organisms associates with histone proteins to organize into an array of nucleosomes. The nucleosome, however, is not one monolithic structure, but rather, refers to an ensemble of assemblies that vary in the chemical modifications present, histone composition, and surrounding DNA sequence. Here, we connect computation with experimental efforts to reveal the effects of acetylation on the H4 histone tail, the impact of a centromere-specific variant on histone assembly structure and dynamics, and the influence of nucleotide sequence on nucleosome breathing. We discover increasing levels of acetylation introduce greater transient order to the H4 histone tail with the mono-acetylation of lysine 16 causing specific structural effects; replacing histone H3 with centromere-specific CENP-A confers enhanced flexibility to dimers and entire nucleosomes, but, interestingly, more rigidity to tetramers; and lastly, that DNA sequences with greater CG content form more stable nucleosomes, undergoing fewer events in which the outer stretches of DNA spontaneously detach and reattach to the histone core.
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